Thanks! I know that I can apply a distance restraint between two atoms in AMBER, can I apply a "repulsive force" restraint between the two atoms (or two residues) directly?
Thanks and best wishes,
Xing
On 07/20/2017 06:23 AM, Elvis Martis wrote:
> HI,
> Not different conformations but slowly pulling apart the dimer by adding restrain potentials to direct them to move away.
> Alternatively, like someone else on the list suggested you can also use SMD.
>
> Best Regards
> Elvis Martis
> Mumbai, INDIA.
>
> ________________________________________
> From: Xing <stecue.gmail.com>
> Sent: 20 July 2017 05:37
> To: amber.ambermd.org
> Subject: Re: [AMBER] pull a dimer apart in AMBER?
>
> Dear Elvis,
>
> Sorry I just saw the reply. Thanks! Do you mean that I can set up a series of different starting conformation in which the distance between the dimer is different and see how stable those
> conformations are?
>
> Thanks and best wishes,
> Xing
>
> On 07/04/2017 11:52 PM, Elvis Martis wrote:
>> HI,
>> Seems possible. You can try umbrella sampling.
>> DOI: 10.1002/wcms.66 this is the reference.
>>
>> Best Regards
>> Elvis Martis
>> Mumbai, INDIA.
>>
>> ________________________________________
>> From: Xing <stecue.gmail.com>
>> Sent: 05 July 2017 07:54:12
>> To: AMBER Mailing List
>> Subject: [AMBER] pull a dimer apart in AMBER?
>>
>> Dear Amber users,
>>
>> I'm trying to "pull" a protein dimer apart in MD, or at least trying to
>> see if the dimer is still stable by applying a pair of force to a
>> certain pair of amino acid residues. Can I do that in AMBER or is there
>> any published literature about that?
>>
>>
>> Thanks and best wishes,
>>
>> Xing
>>
>>
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Received on Thu Jul 20 2017 - 15:00:02 PDT
